Re: [PyMOL] Pymol segmentation fault

[Pete M. <pa...@mc...>]

> Does anyone have any thoughts?

Two things to try that may or may not help:

1. Check if the problem persists when running pymol in single-threaded 
mode ("cmd.set('max_threads',1)").  libpthread in the trace might 
indicate that one of the libraries is having issues with multiple threads.

2. On Kubuntu 8.04.3 LTS x64, I can't reproduce the problem with 1.2 
from svn trunk.  This is using Tcl/Tk 8.4 (with pymol using it's own 
source build of python 2.4.2, which may or may not be relevant); so 
installing Tcl/Tk 8.4 instead of 8.5 (source or binary) might help 
resolve the problem, or at least eliminate one possible source.

Pete

> Here is the backtrace portion from catchsegv:
> Backtrace:
> /usr/lib/libtcl8.5.so.0[0x7f63977b3eb0]
> /usr/lib/libtcl8.5.so.0(Tcl_CreateHashEntry+0x59)[0x7f6397761839]
> /usr/lib/libtcl8.4.so.0(Tcl_FindNamespaceVar+0xff)[0x7f6391d8352f]
> /usr/lib/libtcl8.4.so.0(TclLookupSimpleVar+0xfb)[0x7f6391d9bf0b]
> /usr/lib/libtcl8.4.so.0(TclLookupVar+0xab)[0x7f6391d9b70b]
> /usr/lib/libtcl8.4.so.0(Tcl_SetVar2Ex+0x59)[0x7f6391d9c8e9]
> /usr/lib/libtcl8.4.so.0(Tcl_SetVar2+0x4f)[0x7f6391d9c80f]
> /usr/lib/libBLT.2.4.so.8.4(Blt_Init+0x169)[0x7f6392311859]
> /usr/lib/libtcl8.5.so.0[0x7f639777dee6]
> /usr/lib/libtcl8.5.so.0[0x7f63977102f1]
> /usr/lib/libtcl8.5.so.0[0x7f63977543b8]
> /usr/lib/libtcl8.5.so.0(TclObjInterpProcCore+0x110)[0x7f6397796ed0]
> /usr/lib/libtcl8.5.so.0[0x7f63977102f1]
> /usr/lib/libtcl8.5.so.0[0x7f6397710a5f]
> /usr/lib/libtcl8.5.so.0[0x7f63977926d1]
> /usr/lib/libtcl8.5.so.0(Tcl_PkgRequireProc+0x9)[0x7f6397792209]
> /usr/lib/libtcl8.5.so.0[0x7f6397793192]
> /usr/lib/libtcl8.5.so.0[0x7f63977102f1]
> /usr/lib/libtcl8.5.so.0(Tcl_EvalObjv+0x43)[0x7f6397710413]
> /usr/lib/python2.6/lib-dynload/_tkinter.so[0x7f6398063a32]
> /usr/bin/python(PyEval_EvalFrameEx+0x52fd)[0x4a290d]
> /usr/bin/python(PyEval_EvalFrameEx+0x5837)[0x4a2e47]
> /usr/bin/python(PyEval_EvalFrameEx+0x5837)[0x4a2e47]
> /usr/bin/python(PyEval_EvalFrameEx+0x5837)[0x4a2e47]
> /usr/bin/python(PyEval_EvalFrameEx+0x5837)[0x4a2e47]
> /usr/bin/python(PyEval_EvalCodeEx+0x860)[0x4a40e0]
> /usr/bin/python(PyEval_EvalFrameEx+0x4e4f)[0x4a245f]
> /usr/bin/python(PyEval_EvalCodeEx+0x860)[0x4a40e0]
> /usr/bin/python(PyEval_EvalFrameEx+0x4e4f)[0x4a245f]
> /usr/bin/python(PyEval_EvalCodeEx+0x860)[0x4a40e0]
> /usr/bin/python[0x52bdf0]
> /usr/bin/python(PyObject_Call+0x47)[0x41d6e7]
> /usr/bin/python[0x4254ff]
> /usr/bin/python(PyObject_Call+0x47)[0x41d6e7]
> /usr/bin/python(PyEval_CallObjectWithKeywords+0x43)[0x49c623]
> /usr/bin/python[0x49c06f]
> /usr/bin/python(PyEval_EvalFrameEx+0x52fd)[0x4a290d]
> /usr/bin/python(PyEval_EvalCodeEx+0x860)[0x4a40e0]
> /usr/bin/python[0x52bdf0]
> /usr/bin/python(PyObject_Call+0x47)[0x41d6e7]
> /usr/bin/python[0x4254ff]
> /usr/bin/python(PyObject_Call+0x47)[0x41d6e7]
> /usr/bin/python(PyEval_CallObjectWithKeywords+0x43)[0x49c623]
> /usr/lib/python2.6/lib-dynload/_tkinter.so[0x7f6398061376]
> /usr/lib/libtcl8.5.so.0(TclInvokeStringCommand+0x7f)[0x7f639770e80f]
> /usr/lib/libtcl8.5.so.0[0x7f63977102f1]
> /usr/lib/libtcl8.5.so.0[0x7f63977543b8]
> /usr/lib/libtcl8.5.so.0[0x7f63977527b9]
> /usr/lib/libtcl8.5.so.0(TclEvalObjEx+0x196)[0x7f6397711706]
> /usr/lib/libtk8.5.so.0[0x7f6397a556f6]
> /usr/lib/libtcl8.5.so.0[0x7f63977102f1]
> /usr/lib/libtcl8.5.so.0(Tcl_EvalObjv+0x43)[0x7f6397710413]
> /usr/lib/libtcl8.5.so.0(TclEvalObjEx+0x300)[0x7f6397711870]
> /usr/lib/libtcl8.5.so.0[0x7f639779668f]
> /usr/lib/libtcl8.5.so.0[0x7f63977102f1]
> /usr/lib/libtcl8.5.so.0[0x7f63977543b8]
> /usr/lib/libtcl8.5.so.0(TclObjInterpProcCore+0x110)[0x7f6397796ed0]
> /usr/lib/libtcl8.5.so.0[0x7f63977102f1]
> /usr/lib/libtcl8.5.so.0[0x7f6397710a5f]
> /usr/lib/libtk8.5.so.0(Tk_BindEvent+0x890)[0x7f6397a29c90]
> /usr/lib/libtk8.5.so.0(TkBindEventProc+0x185)[0x7f6397a2fa35]
> /usr/lib/libtk8.5.so.0(Tk_HandleEvent+0x6c0)[0x7f6397a374c0]
> /usr/lib/libtk8.5.so.0[0x7f6397a37b48]
> /usr/lib/libtcl8.5.so.0(Tcl_ServiceEvent+0x7f)[0x7f639778764f]
> /usr/lib/libtcl8.5.so.0(Tcl_DoOneEvent+0x8f)[0x7f63977878ff]
> /usr/lib/python2.6/lib-dynload/_tkinter.so[0x7f639805f201]
> /usr/bin/python(PyEval_EvalFrameEx+0x52fd)[0x4a290d]
> /usr/bin/python(PyEval_EvalCodeEx+0x860)[0x4a40e0]
> /usr/bin/python(PyEval_EvalFrameEx+0x4e4f)[0x4a245f]
> /usr/bin/python(PyEval_EvalCodeEx+0x860)[0x4a40e0]
> /usr/bin/python(PyEval_EvalFrameEx+0x4e4f)[0x4a245f]
> /usr/bin/python(PyEval_EvalCodeEx+0x860)[0x4a40e0]
> /usr/bin/python[0x52beed]
> /usr/bin/python(PyObject_Call+0x47)[0x41d6e7]
> /usr/bin/python(PyEval_EvalFrameEx+0x3921)[0x4a0f31]
> /usr/bin/python(PyEval_EvalFrameEx+0x5837)[0x4a2e47]
> /usr/bin/python(PyEval_EvalFrameEx+0x5837)[0x4a2e47]
> /usr/bin/python(PyEval_EvalCodeEx+0x860)[0x4a40e0]
> /usr/bin/python[0x52bdf0]
> /usr/bin/python(PyObject_Call+0x47)[0x41d6e7]
> /usr/bin/python[0x4254ff]
> /usr/bin/python(PyObject_Call+0x47)[0x41d6e7]
> /usr/bin/python(PyEval_CallObjectWithKeywords+0x43)[0x49c623]
> /usr/bin/python[0x4d0c4d]
> /lib/libpthread.so.0[0x7f639cf69a04]
> /lib/libc.so.6(clone+0x6d)[0x7f639c4317bd]
> 
> Thanks,
> Ian
>